Proteomics for Biomarker Discovery

There are three common proteomics study designs for biomarker discovery with dominant differences in the proteome coverage, sensitivity, and throughput (Figure 3):

◆ Discovery (shotgun) proteomics approaches have high coverage of proteome (up to 10,000 proteins in a single sample), but at the expense of throughput. High-resolution mass spectrometry (Orbitrap or time-of-flight instruments) is the representative technology platform of shotgun proteomics experiments.

◆ Targeted discovery approaches focus on a panel of high-potential proteins in sufficient numbers of samples. The coverage depends on the size of the panel or array used. The available technology platforms include antibody-based protein arrays, aptamer-based protein array, data-independent acquisition mass spectrometry, etc

◆ Targeted proteomics is the most sensitive approach that allows the detection of low-abundance markers such as interleukin (IL)-6, but is limited in coverage and throughput. The available technology platforms include ELISA panels, multiple-reaction monitoring mass spectrometry (triple-quadruple instruments), etc .